1. Technical Field of the Invention
The present invention generally relates to the fields of imaging and scanning. In particular, the present invention provides scanning systems and methods for high speed scanning and imaging of a sample containing labeled materials, for example scanning arrays of polymer sequences such as oligonucleotide arrays.
2. Description of the Related Art
Polymer arrays, for example, DNA arrays, are known as shown in patent application U.S. Ser. No. 08/811,829 (""829) and U.S. Pat. Nos. 5,744,305; 5,445,936; and 5,677,195; which are hereby incorporated by reference in their entirety for all purposes. The polymer arrays, such as the GeneChip(copyright) probe array (Affymetrix, Inc., Santa Clara, Calif.), can be synthesized using light-directed methods described, for example, in U.S. Pat. Nos. 5,143,854; 5,424,186; 5,510,270; and PCT published application no. WO 95/11995, which are hereby incorporated by reference in their entirety for all purposes. In one method, an array containing synthesized single stranded nucleic acids such as DNA, is enclosed in a protective package, as shown in patent applications U.S. Ser. Nos. 08/528,173 and 08/485,452 which are hereby incorporated by reference in their entireties for all purposes. The array is contacted with a sample containing single stranded DNA that is labeled using for example fluorescent labels such as fluorescein or phycoerythrin, and which hybridizes to the single stranded DNA on the array. After hybridization, the array (either packaged or not packaged) is placed into a device generally known as a scanner that obtains a fluorescence image of the array in order to analyze hybridization between the single stranded nucleic acids on the array and in the sample.
Systems (scanners) and methods for detecting marked targets on polymer arrays are generally known. Typically the polymer array is scanned using a scanner that directs a point of light in a rectilinear raster fashion so as to image the entire polymer array. A scanner may include a confocal microscope with a light source for generating light directed to the polymer array, a photodetection mechanism for detecting light emitted from the polymer array, and a computer controlled translation table that moves the polymer array in three (XYZ) directions. One direction is the fast scan direction (e.g., X direction), another is the slow scan direction (e.g., Y direction) and the third direction is a focus direction (e.g., Z direction).
As an example, the scanner projects a point of light onto a surface of the polymer array and is focused by the translation stage in the focus direction; Z direction. Next, the translation stage rectilinearly fast scans the point of light from one side of the polymer array to another by moving the polymer array in for example the X direction, so as to scan one line of the polymer array, point by point. During the fast scan the photodetection mechanism detects the light emitted from the surface of the polymer array so as to obtain a fluorescence image of the polymer array. Once one line in the fast scan (X) direction has been scanned the translation table moves the polymer array incrementally approximately the thickness of one scan line in the slow scan (Y) direction. This raster scanning continues until the entire surface area of the polymer array has been scanned. (See for example U.S. Pat. No. 5,631,734 issued to Stern et al., which is hereby incorporated by reference in its entirety for all purposes.)
There is a need for a polymer array scanner which is reasonable in cost and provides high polymer array scanning throughput and high resolution, e.g. 1.5 xcexcm 3.5 xcexcm, or smaller pixel size over a 14 mmxc3x9714 mm field.
The present invention provides systems and methods for image scanning of, for example, polymer arrays. The invention provides means for moving a linear translation stage of a scanning system with a speed of at least 10 scanning lines/second, preferably at least 20 scanning lines/second and more preferably at least 30 scanning lines/second over a scanning distance of at least 2 mm, preferably at least 5 mm, and more preferably at least 14 mm. The scanning system is capable of scanning with pixels having a size of approximately 3.5 xcexcm or less, preferably having a size of approximately 2 xcexcm or less, and more preferably having a size of approximately 1.5 xcexcm or less, while maintaining the fast scanning speeds indicated above and accurately detecting an image. In some embodiments, the scanner includes a voice coil to provide scanning motion for at least one of the X direction, Y direction, and Z direction translation of a polymer array analysis system. The acceleration of the voice-coil-driven axis of the present invention is high (e.g., 13.7 G, where G is the acceleration due to gravity) and can not easily be achieved with stepping motors. The high acceleration, combined with the high steady-state scan speed of the voice-coil-driven axis (about 22 inches/second), enables the voice coil scanner of the present invention to scan a distance of, for example, 14 mm (length of scan line of one type of polymer array) at 30 lines/second.
The voice coil scanner of the present invention can use either stationary optics or a moving scan head. In either case, the voice-coil-driven axis is the X axis. In one embodiment, the voice coil drives a lightweight linear slide mounted on a 2-axis (YZ) translation table. This linear slide serves as the support for a polymer array (scanned sample). In another embodiment, the voice coil drives a scan head, i.e. a lightweight linear slide that supports a turning prism or turning mirror and an objective lens, while the polymer array is supported by the 2-axis (YZ) translation table. Further, a motion control system is provided to monitor and control the motion of the voice coil for fast accurate scanning of the polymer array.
Using a voice coil for high speed scanning of polymer arrays in the fast axis (X) direction, rather than using a galvanometer driven scanning mirror, enables the use of a simple low cost objective lens having a high numerical aperture (for example, 0.5 or greater). The objective lens can be, for example, a microscope objective lens or a single element aspheric lens. This objective lens can have high numerical aperture while being small and inexpensive because it does not have to be corrected for off-axis aberrations, unlike the objective lens in a galvo scanner. All other things being equal (laser power, spot size, etc.), a scanner with an objective numerical aperture of 0.5 operating at 30 lines/second produces images with the same signal-to-noise ratio as a scanner with an objective numerical aperture of 0.25 operating at 7.5 lines/second.
As a result of using the combination of a voice coil driven translation stage and a simple high efficiency objective lens, the voice coil scanner of the present invention can achieve fast scanning and high polymer array throughput. For example, the voice coil scanning system of the present invention, with an objective lens having a numerical aperture of 0.5 or greater, can achieve accurate and reliable polymer array scanning at a speed of at least 10 lines/second, preferably at least 20 lines/second and more preferably at least 30 lines/second.
Therefore, the present invention provides a scanning system with a simple and inexpensive objective lens and a high acceleration/high speed voice coil driven translation stage that can rapidly scan, for example, 12.8 mmxc3x9712.8 mm polymer arrays using a pixel size of, for example, about 3.5 xcexcm or smaller, more preferably 2 xcexcm or smaller and most preferably 1.5 xcexcm or smaller. The voice coil provides improved acceleration for fast scanning of at least one axis of a polymer array. As a result, the present invention provides systems and methods for accurate, high speed, low cost scanning of polymer arrays, i.e., high performance cost effective polymer array scanning.